The Second Hour
by The Pygairian
Summary: Suppose it wasn't the doctor's eleventh regeneration that crash landed in the Pond's yard. Suppose it had been a different bow tie wearing Doctor. And then suppose he had never regenerated before either, and things weren't quite happening as they were supposed to.
1. The Second Hour Pt 1

He blinked, for the first time, his eyes watering. As his brand new eyes came into focus, they were met by things falling around him and flying sparks. _Was that the ground shifting, or only his new unsteady legs?_

He recognized the round shapes all around him. TARDIS. This was the TARDIS.

The room seemed to rock back and forth, suddenly. As he stumbled, the controls seemed to reach out to him, breaking his fall. There was a soft humming in the back of his mind that was somewhat familiar and comforting, but also seemed strained.

He gasped as his new ears became aware of the chiming bells coming from deep within his ship. That was bad. He knew that, but he couldn't remember why. In fact, he could hardly remember anything.

He knew that couldn't be right. At the academy, they always told him he would remember everyth-

His mind went blank suddenly. He shook his head. He must remember someth-

No, this couldn't be right. It was as if he had some sort of mental interference. Like white noise in his head that kept interrupting his thoughts.

He took a moment to admire the comparison.

His ship shuttered again. He nearly fell to the floor, his new limbs awkward and stiff.

His eyes rested on a big red button labeled, with a sticky note, "Emergency Landing". He smiled slightly at his own foresight and pressed it.

* * *

Amelia was new to England. She had seen and heard many unusual and foreign things since she moved here, but this was by far the strangest.

The strangled groaning sound seemed to phase in and out of existence. It was almost magical sounding, so strange, but also inviting. Yet it seemed strained, as if under pressure or in pain if a sound could be in pain.

She gently brushed her curtain aside. Outside, in her front yard, stood a large blue box. It had words on it, though through the thick smoke billowing out of the box she couldn't make them out.

Amelia's heart pounded with excitement. What could this be? A sense of adventure filled her heart. Quickly, she grasped her large flashlight and headed downstairs.

Once outside, she became somewhat less enthusiastic. What if it was dangerous? What if it was a bomb? Or Aliens?

She brushed that idea away quickly. It was ridiculous. Besides, as she could now see, the words on the side were English. Why would an alien use English? And it said Police.

She took a startled step back as the door swung inward. Out of the smoke stumbled a man, average height. His clothes were dirty and torn and he held an old handkerchief over his face. As soon as he got clear of the smoke, he removed it and sighed. Looking around, he seated himself on one of the garden rocks.

"Great jumping Gobstoppers. Only been here a few hours and I've already made a mess of it." He grumbled to himself. "The ship's a mess and I have no idea where I am. A fine way to start a new life." The man mopped his forehead with the handkerchief and then put it back in his pocket.

"Mister..."

The man nearly jumped out of his skin when Amelia spoke. He turned quickly but smiled when he saw her.

"Well, well, well! Hello there!" he said, grinning. He clapped his hands together. "I do hope you'll forgive my appearance. You see, I've just gone through a rather harrowing experience."

At harrowing, he frowned. "I wish I could remember what happened." The smile returned. "Ah well. Just a bit of post renewal amnesia. I'm sure it will all come back with t-..."

He suddenly broke off, clutching his side as if in pain. His face twisted for a moment, and he stumbled to his knees.

"Are you alright, mister?" Amelia asked, concern on her face.

"I... I believe so. Just a little trama from the renewal. It's a difficult thing, you know. Becoming a new man and all. Still cooking on the inside, I think." He gasped as if he was short of breath.

"Are you a policeman?"

The man looked at her, suddenly confused. "A policeman? No, of course not. Whatever gave you that idea?"

"Y-your box. It says police on the side."

"Yes. I never did get to fixing that chameleon circuit."

"Did you come about the crack in my wall?"

"A crack?" This seemed to pique his interest. "What crack?"

"Come on. I'll show you."

* * *

The man, who she now knew called himself 'The Doctor', stood back, examining the crack. He held in his hand a small black book with strange circle symbols on the cover. He hadn't said a word, only thumbing through his book, and frowning.

When he finally did speak, it caused Amelia to jump.

"Well!" he said, suddenly. "There are no two ways about it... It seems some one or something has been meddling in the space time continuum. It's a wonder _They_ haven't caught on yet..." he rested a hand on his chin.

"What do you mean?" Amelia asked.

"I mean that this crack isn't an ordinary crack. It's very special, and... It could be very dangerous..." The Doctor frowned.

"Dangerous?"

"Oh, yes. A rift in the space time continuum could lead to all sorts of..." Doctor seemed to suddenly realize who he was talking to. "... Well... don't worry, my dear. I'll just close it up again, shan't I?"

Amelia nodded.

"Now, let's see..." The Doctor began searching through the pockets of his ragged clothing. He pulled out a small object that resembled a penlight. An odd look came over his face. "A Sonic screwdriver? I don't remember... I wonder where I got this...?"

"What's a Sonic screwdriver?" Amelia asked.

"It's a highly scientific device that uses sound waves to do... well, a lot of things that I don't really have time to explain. What's important is that I can use it to close the crack if I can find the right frequency..." he carefully laid his ear against the crack.

His face changed. "Oh dear."

"Do you hear the voices?" Amelia asked, anxiously.

"Yes..." the Doctor frowned as if listening. "But what are they saying? I can't quite make it out..."

He pressed his ear closer. "Pri... prisoner... is that Nero, or Zero? E... escaped? Prisoner... Zero... has... escaped..."

"I heard that too. What does it mean?"

The Doctor stayed quiet a moment. "I suppose it means that this crack leads to a prison and someone, presumably Prisoner Zero, has escaped. Which can't bode well for us..." he added, quietly, resting a hand on his chin.

"What do we do?"

"I'll start tuning this sonic screwdriver to the correct frequency. It should take some time though. Why don't you go make some sandwiches while I work on this?" He smiled warmly. "Sometimes a sandwich can make all the difference."

Amelia couldn't help smiling back before she went downstairs to get started.

* * *

AN: I hope you've enjoyed this so far. this is a rewrite of my previous story called "The second hour". I recently reread the other one and I wasn't satisfied with it, so here it is again, new and improved.

I'm planning on doing a whole series in this one that will answer questions like "Why did theDoctor regenerate?" and "What ever happened to Ben and Polly?". I intend to write a whole story arch.

Anyway, I hope you enjoyed it so far. any feed back is very welcome!

The Pygarian


	2. The Second Hour Pt 2

When Amelia returned with a plate of sandwiches, the Doctor looked as if he hadn't moved. He still had his ear pressed up against the wall, but now he held up the sonic screwdriver, as if listening to both. He seemed deeply concentrated, pressing the button on the side of the screwdriver every now and again, letting out a gentle whirring sound. Amelia couldn't pick out any change each time, but she could hear him mutter something about "too low", or "a little sharp". Finally, he seemed satisfied.

"There. That should do it." He turned, and suddenly his face lit up. "Oh, good! You've finished the sandwiches!"

He clapped his hands together happily, a wide grin on his face. He slipped the screwdriver into his pocket, and care fully picked one up. "There's nothing like a sandwich to solve the problems of the universe."

He took a bite, and then turned back to the crack. "I think I've got it. If I resonate the correct frequency, it should invert the forces and the crack will close. Of course..." He trailed off, glancing at Amelia.

"What? Is something wrong?"

"No. I mean, don't worry. I... I know what I'm doing..." The Doctor smiled, though it didn't seem very reassuring. "Just stay behind me, there's a good girl."

He pulled the Sonic screwdriver out of his pocket, and pressed the button.

At first, nothing seemed to happen. Then the crack began to open wider. Behind it was a deep darkness. They could hear the voice easily now.

"Prisoner zero has escaped."

"Hello?" The Doctor said, carefully.

Very suddenly, what appeared to be a very large eye appeared.

Amelia started backward.

"Oh my giddy aunt..." The Doctor swallowed.

The creature observed them for a moment before, just as the crack began to close again, it sent a blue bolt of light hitting the Doctor's pocket. He stumbled back slightly.

"Are you okay?" Amelia asked, glancing over at where the crack had closed seamlessly.

"I'm alright." He pulled the black book out of his pocket and opened it. The pages were glowing blue.

"Prisoner Zero has escaped..." he slowly read aloud. "But... why tell us?" He rested a hand on his chin and frowned. Then he sighed, shaking his head. "It's difficult, really. You see, I've never done this before, and my mind is still quite a bit muddled."

Amelia frowned. "Never done what?"

The Doctor seemed to see her for the first time. "Oh... Nothing. Just a little post renewal confusion."

He smiled warmly. "How about another sandwich?"

He offered the plate to her and then carefully picked up another triangle of bread and took a bite. "Where are your parents, Amelia?"

"I don't have any." She looked down. "Just an aunt."

"Oh. I'm sorry." The Doctor chewed thoughtfully for a moment. "I used to have an aunt..."

His eyes drifted around her room and settled on something on her desk. Seemingly entranced, he walked over and picked it up. "What is this?" He asked.

"That's a recorder. I have to play it in my music class in school. It's rubbish."

The Doctor's eyes lit up. "You know, I was given one of these by King Henry the VIII. He had quite a collection, you know."

"But he lived hundreds of years ago." Amelia argued. "How could you know him?"

"My ship can travel through time." He said absently, still inspecting the instrument.

"Your ship?"

"Yes." The Doctor took another bite of his sandwich. He closed his eyes as if thinking.

"Doctor..."

"What does it all mean?" The Doctor said, suddenly very animated. He began muttering quietly, and pacing. He paused, and then left the room, going down the stairs.

Amelia followed him, not sure what he was doing. She followed him right to the door of his box.

The smoke coming out was less than it had been, yet the Doctor seemed surprised when he saw it.

"What happened to my ship?" he said to himself.

"This is your ship?" Amelia said, skeptically. "But its a box!"

"Of course it is!" The Doctor frowned. "But why is it damaged?"

"Don't you remember? It was that way when you came here."

"Was it?" He frowned. "It must be the temporal linking system... I must repair that immediately. Just a little hop to the future should do it." He opened the door, but stepped back as more smoke billowed out.

"It's worse than I thought." The Doctor pulled his handkerchief from his pocket and plunged into the wall if smoke.

Amelia watched after him a moment, and then called "Doctor?"

She started back as he suddenly emerged from the smoke.

"I have to go, my dear." He said, kneeling so that he could be the same hight as her. "But don't worry. I'll be right back."

Amelia looked down. "People always say that..."

The Doctor smiled, a touch of sadness in his face. "Don't worry. I'll return as quickly as I can. Trust me."

Amelia smiled slightly. "Okay."

He patted her on the arm gently, and then turned and disappeared into the smoke. a moment later, Amelia heard the same strained groaning sound, and the box began to phase in and out of existence. A moment later, it was gone, only the smoke lingering in the air suggesting that it had ever been there at all.

* * *

The sun was high in the sky, it's rays warming the earth. The trees were swaying gently in the light breeze, and somewhere in the distance, a bird could be heard, singing it's sweet song.

The peace was suddenly interrupted by a harsh wheezing sound. The tall blue shape of the Tardis began to phase in and out of reality, somehow making a slight wind pick up.

Smoke still poured from inside, but it gently floated downward and settled around the Tardis base.

The door opened, suddenly, sending out a large billow of smoke.

The Doctor stumbled out, covering his mouth with his handkerchief. In his other hand, he held a long thin object.

"Amelia!" He called, excitedly, holding it up. "I found my recorder!"

He paused as he observed his surroundings, and he frowned. "Oh dear. I must have been longer than I thought. Amelia?" He approached the door, and found that it was locked.

"Hello? Amelia?" No one answered his knocking.

He sighed and sat down on the step outside_, _putting the recorder to his lips and playing a gentle tune.

_Prisoner zero has escaped. Why go through all the trouble to tell us? What does it all mean? What was that crack? _

Suddenly, it clicked. "Oh my giddy aunt! Prisoner Zero is here!" he said, suddenly standing.

"Who are you?"

The Doctor turned toward the voice suddenly, startled. He smiled, gently. "I beg your pardon, ma'am, but you wouldn't by chance know the people that live here, would you? It's very important."

The young woman wore a police uniform, and she had striking red hair pulled into a tight bun.

"Why do you want to know?" Her voice had a distinctly Scottish accent.

"Well, you see, who ever lives here is in great danger. There is a dangerous alien convict hiding somewhere in this area, likely in the house."

The policewoman stared at him, dubiously.

"If you don't believe me, ask the girl, Amelia. She can tell you my story is true, but it's viral we do something now before it's too late."

"Amelia Pond?"

"Yes." The Doctor sensed a bit of disbelief. "She does live here, doesn't she?"

"Amelia Pond hasn't lived here in a long time."

The Doctor froze. "What?" he said, in disbelief. "But... how long?"

"...Six months."

"...What?" The Doctor's eyes widened, and he gaped. "But it can't be... I told her I would be back in only a moment. I knew I went a bit far, but... six months? Are you entirely sure?"

The policewoman frowned. "Listen, Mister, I don't know who you are, but this is private property."

"Listen, I must speak to whoever lives here. It's very important."

"I live here."

"I see. Well," he smiled slightly, "first off, what's your name?"

"R-Rachel. Rachel... McLaren."

The Doctor's brow furrowed slightly. "Miss McLaren, six months ago, I was here with Amelia Pond. There was a space-time crack in her wall, and I fixed it for her. What I didn't realize at the time was that that crack had allowed a dangerous alien life form to escape from a high security prison and hide in this house. Now everyone around here is in grave danger."

The policewoman frowned. "That's ridiculous!"

"If you would allow me inside, I would prove it to you." The Doctor sighed, exasperatedly.

"I don't even know you."

The Doctor grumbled slightly, saying something about not being listened to. "You don't seem to understand! This is a matter of life and-..."

"Prisoner Zero will vacate the human residence, or the human residence will be incinerated."

The policewoman nearly jumped out of her skin as the voice suddenly echoed through the air. "What's that?!"

"I tried to warn you! We need to get out of here!" He grasped her hand, and pulled her away, toward the Tardis. She was too stunned to argue.

"Prisoner Zero will vacate the human residence, or the human residence will be incinerated."

The Doctor fished the key out of his pocket and shoved it into the lock, only to find it wouldn't turn. "Oh dear. She won't let me in!" He pounded on the door in frustration.

"What's going on, Doctor?!"

The Doctor turned toward her. "My ship is repairing itself and won't let us in, and there are aliens that want to incinerate your house. I'm afraid I can't explain any further than that right now, though." He was going to try the door again, but the police woman grasped his wrist suddenly, yanking him away and forcing him to turn toward her. "Tell me what's going on!"

"I-..." He was cut off as the door to the house suddenly opened.

Standing in the doorway was a man holding a dog by a leash. He looked around for a moment, his dog creepily dog he same in sync, before he looked at them. The dog started growling, but... then they realized that it wasn't the dog but the man.

The policewoman stood, staring. "What... What?!"

The Doctor had his small black book out again. "Multiform..." he frowned. "Got the voice a bit muddled though. Long way from home aren't we?" He said to the "man".

The man and dog stepped forward, suddenly, growling again.

The Doctor stepped back, taking a sharp breath. "Now, there's no need for violence. I'm sure we could settle this civilly."

Prisoner Zero suddenly opened it's mouth, displaying large needle-like teeth.

"I guess not." The Doctor turned to the policewoman, though he didn't take his eyes off Prisoner Zero. "When I say run..." He took her hand, "...Run!"

The Doctor pulled her along with him, suddenly.

The policewoman stopped, as soon as they slowed. "I want answers from you."

The Doctor winced at her harsh tone. "I-..."

"I find you sitting outside my house, looking like you walked through a hurricane, and then you say there are aliens, and my house is going to be incinerated-..."

"Please! If you would only allow me to explain."

She didn't protest, only glaring at him.

"First off, I am the Doctor..." He got a peculiar look on his face. "But this is the first time I've said that." He turned to her, suddenly suspicious. "How did you know who I was?"

She seemed suddenly flustered. "I-I must have... You must have mentioned it some time."

"I can assure you, I did not." He looked at her, his dark eyes searching hers. "How did you know that?"

She looked slightly panicked, and blurted out, "Well, why did you say just a moment!"

The Doctor's eyes widened in shock. "No... Amelia?"

* * *

AN: I hope you've enjoyed this so far. I'm hoping to finish this adventure in one or two more chapters. Then we can dive into their future adventures. I have some exciting ideas for the future stories.

Please, tell me what you think!

Happy writing and reading!

The Pygairian


	3. The Second Hour Pt 3

"It's Amy now."

"What?" The doctor appeared to be somewhat stunned.

Amy clenched her teeth. "I've waited twelve years for you to come back! Twelve years!"

The Doctor flinched slightly. "Oh dear. I really am very sorry... My ship was damaged. It was an accident."

"I had four psychiatrists!"

"Four?"

"I kept fighting them. They said you weren't real."

The Doctor opened his mouth to say something and then seemed to think better of it, instead looking down at the ground.

"Prisoner Zero will vacate the human residence, or the human residence will be incinerated."

The Doctor looked up, suddenly. The voice was coming from a nearby ice cream van.

"What? We're being staked out by an ice cream van!" Amy seemed slightly panicked.

The doctor sprinted over to the van. "Excuse me, old fellow," he said to the attendant, "But why are you playing that?"

The confused man shrugged. "It's supposed to be Clare de lune."

The Doctor frowned, stepping away from the van. He rested a hand on his chin. "So it isn't only her house..." he muttered to himself. "But what do they mean? The town? The country? Perhaps even the whole world?" He furrowed his brow.

Suddenly a shadow passed over them.

"Doctor, what's going on?" Amy asked, looking up. "What's wrong with the sun?"

"It's worse than I thought." The Doctor frowned. "The sun... That's what it looks like through a force field. It seems the Atraxi meant more than just your house."

He shielded his eyes and looked at the sky. "They've got to warm up the ship before they could do any damage... even if we're lucky, we've only got twenty minutes!" His face suddenly filled with worry.

"What are the Atraxi? Twenty minutes until what, Doctor?" Amy asked, in vain.

The Doctor began searching through his pockets. "I must have something-... Agh!" he suddenly broke off in a cry of pain, and spasmed, collapsing to the ground. His face contorted in pain, and he spasmed again.

"Doctor!" Amy knelt by him. "Are you okay?"

"Amy!" A young man in a nurse's scrubs came running over, kneeling by the Doctor. The few people who weren't too distracted by the sun stopped and looked.

"Rory!" Amy said, recognizing the young man.

"What happened?" Rory asked.

"I don't know! He just collapsed!" Amy looked down at the Doctor. He was clutching his head and taking deep breaths. "Doctor? Can you hear me?"

The Doctor blinked and suddenly sat up. He looked at them, a look of genuine confusion on his face. "My goodness! What are you two doing down here?" He stood up and dusted himself off as if nothing had happened.

Amy and Rory stood back, confused.

"Sir, I need you to sit down," Rory said. "I'm a nurse, and you're not well."

"Not well?" The Doctor frowned. Then a knowing grin spread on his face. "Oh... Oh, I see. No, you don't need to be worried about that little... I mean, it's only post renewal side effects. It's all really perfectly normal." He turned and started walking away, leaving the two of them standing there, baffled.

Amy recovered first. "Doctor!" She followed after him. "Wait!"

The Doctor looked around at the surrounding town. "Amelia, is there any sort of science station here? A nuclear plant? Perhaps a hospital?"

Amy grasped his wrist, suddenly slapping cold steel around it.

"What the-...?" Suddenly, the Doctor found his wrist was handcuffed. On further inspection, he found it was handcuffed to Amy's wrist.

"Amelia, what are you doing?" His eyes widened. "Where did you-...?"

"I want answers." She said, her jaw clenched. "Who are you?"

"You know who I am! Amelia-..."

"Amy."

"Amy, what are you doing?" Rory caught up to her.

Amy ignored him. She looked the Doctor in the eyes. "I know what you call yourself, but who are you really? What did you mean by we have twenty minutes?"

"Amelia-... Amy, you know who I am. I'm the Doctor. In twenty minutes, the entire planet is going to be incinerated by the alien race, the Atraxi, and I have to do something about it, so if you would uncuff me now..."

"No."

"What?"

"No!" Amy yanked him closer, grasping his shirt. "I want the truth! What are you really? A con man? An escapee from an insane asylum?"

The Doctor looked panicked. "No, no, no, of course not! You don't understand! The whole planet is at stake! Don't you see? And every second that passes reduces the chances of my being able to do anything about it! Please, uncuff me!"

"Amy, is that him? The raggedy Doctor?" Rory asked.

"Shut up, Rory!" She hissed. "I'm not a child, Doctor. I don't fall for that stuff anymore."

The Doctor looked exasperated. "You believed me when I fixed that crack in your wall. Why don't you now? Don't you remember?"

"I grew up! I realized that disappearing boxes that can time travel and aliens that look like giant eyes are stupid imaginary fantasies of my childhood. But then you show up again."

The Doctor sighed. "I don't expect you to take my word, but you've seen it with your own eyes! Prisoner Zero! And look at the sun! Even if you don't believe me, please, _try_ to do so. Just for twenty minutes. After that, I'll explain everything and you can curse me, forget me, even arrest me, and I won't blame you, but not before then. Please!"

Amy looked him in the eye. She seemed to be struggling with herself. Finally, she sighed. "Fine. Twenty minutes."

The Doctor smiled. "Would you be so kind as to uncuff me now?"

Amy reached in her pocket, and her face went white. "I... The key... I must have lost it..."

"Lost it?! How could you have lost it!?" The Doctor said, exasperatedly. "Oh, nevermind. We don't have time." He turned to Rory. "Rory is it? Do you have a science station here?"

Rory shook his head. "We have a post office and a hospital."

"Ah. A Hospital. That will have to do. Do you have a motorcar, Rory?"

"Y-yeah. It's over there."

"Is it automatic?"

"No, it's a manual."

"Come on, Amy." The Doctor dragged her toward the car by the handcuffs while glancing at a battered watch on his uncuffed wrist. "Only seventeen minutes left. Come along, Rory! If your car is a manual, you'll have to drive. You're the only one with two hands!"

* * *

As soon as they arrived at the hospital, the Doctor dragged Amy inside, followed closely by Rory. The hospital staff cast them strange looks as they passed, and whispered.

"What are they looking at?" The Doctor asked Amy, quietly.

She only cast him a confused look.

"Rory, is there a coma ward?"

"Yeah, I work there."

"Good."

The Doctor led them down the corridor the Coma Ward. As soon as they were inside, he began collecting pieces of unused equipment and taking them apart.

"Hey, that's Hospital property." Rory half-heartedly said.

"Yes, it is, isn't it?" The Doctor began piecing parts together and messing with the equipment. "Amy, do try to keep your hand out of the way, will you? After all, this is partially your fault." He frowned. "Did you really have to handcuff me?"

Amy's face turned a shade of pink, and she looked away.

"Rory, could I borrow your mobile phone?"

"Sure." Rory handed the phone over, somewhat warily.

The Doctor pulled out his sonic screwdriver and continued. "If I've wired this correctly," He said, stepping back from the strange contraption he had created, "With the addition of this power crystal from Stike 5, it should send a powerful signal. Hopefully, the Atraxi will pick it up on their sensors and be attracted here. Then perhaps I can have a little talk with them, and avoid the destruction of the earth."

"It is too late for that, Doctor..."

The Doctor turned, suddenly, coming face to face with a middle-aged woman standing between them and the door. "The Atraxi will never find me."

"Prisoner Zero, I presume." The Doctor's face was cold and calculating. "I don't suppose you would simply surrender, would you? That would make this whole business much easier for both of us."

"The Atraxi will kill me this time." The lady cocked her head in an unsettling way. "If I must burn, I will take the people of earth with me."

The Doctor frowned and rested a hand on his chin. "Oh no. I'm afraid I can't allow that."

"Why should you care? You are not of this world."

"I suppose not, but I've grown rather fond of it. It is one of my favorites."

"No matter." Prisoner Zero smiled slightly. "You will die with it then, Doctor."

"I think that is where you're wrong." The Doctor connected two wires on his contraption and suddenly there was a high pitched ringing sound. The lights in the room sparked and burnt out.

"What are you doing?!" Prisoner Zero shrieked.

"Doctor!" Amy cried out.

"Its the end for you, Prisoner Zero." The Doctor said, his face stern. "When the Atraxi scan this hospital, they will find only two non-humans. You, and me. You can hide your shape, but not your DNA. They couldn't possibly confuse a Time Lord with a Multiform."

"Then you will die with me, Doctor!" Prisoner Zero very suddenly leaped at the Doctor, catching him by surprise and slamming him to the floor. Amy was yanked down with them.

The Doctor shoved it off of himself and stood, pulling Amy behind him. "When I say run..." He said quietly to her, but before he could act, Prisoner Zero was on him again, shoving him into some equipment and pinning him. It opened its mouth, showing off long fangs, but before it could attack, a blue light began forming around it and the Doctor. Suddenly, they vanished, leaving Amy sprawled on the floor, the chain of the handcuffs broken.

* * *

The Doctor felt his body go numb, and his vision went grey. After a moment, as his vision came back, he found himself standing in the bridge of what seemed to be a starship. In front of him was what looked like a massive eye.

"Who are you?" The Atraxi asked, its voice vibrating in the Doctor's skull.

"I am someone who doesn't like seeing an entire planet of innocent people destroyed through carelessness. Do you realize the consequences of what you were about to do? Destroy a level five civilization? Billions would have died!"

"You are not of that world."

"Does that matter?" The Doctor straightened up a bit, trying to appear taller. (Over the course of the day, he had realized that this body was significantly shorter than his previous.) "Do you realize what would happen if I were to tell someone about this little mishap? The shadow proclamation? Article 57. Of course, If I were in a particularly nasty mood, I might even tell the Celestial Intervention Agency. I can only imagine what _T__hey _would do if they found out." The Doctor clapped his hands together, smiling grimly. Then his smile turned whimsical. "Of course, as no one was actually hurt, I might be willing to overlook this, so long as nothing like it ever happened again."

The Doctor chuckled, but then turned more serious. "I would choose wisely if I were you."

* * *

It had only been a few minutes when a blue light began to form in the Coma Ward again. The Doctor reappeared slowly, and then the light disappeared.

"What happened?" Amy asked, still dazed from the fight with Prisoner Zero.

"I had a talk with them." The Doctor grinned. "You don't need to worry about them anymore. And I'm sure you'll find the sun is back to normal." He quickly walked out of the room.

"Wait! Doctor!" Amy quickly picked herself up and followed after him.

When she got into the hall, there was no sign of him. A sudden fear hit her heart. She breathed in sharply and then ran to her house as fast as she could. She got there just in time to see the blue box fading in and out of existence.

* * *

A whirring, wheezing sound echoed through the still night. The old house was quiet, though a single room was still lit.

The imposing shape of the Tardis began to materialize on the grass.

The door to the house opened, and Amy rushed out. She stopped short, her eyes wide when she saw the box standing there.

The door opened, and the Doctor came out. He looked as if he had tidied himself up a bit. His hair, though still it refused to represent a hairstyle, was combed. He wore a somewhat oversized black frock coat, with a red handkerchief in the pocket. He had a new shirt on that was light blue, and a pair of striped brown and black trousers. Haphazardly pinned to his collar was a navy blue bowtie with white polka dots.

"Sorry I popped off so fast earlier." He said, smiling. "My ship needed a test run after all the repairs she had to make."

"It's you..."

"Yes. I know I owe you an explanation about it all, and I had a question to ask you."

"Everything that happened, with Prisoner Zero and the Atraxi... That was two years ago!" She shouted.

The Doctor grimaced. "Great jumping gobstoppers... Not again. I'm terribly sorry."

They stood in awkward silence for a moment.

"You changed your clothes," Amy said, after a moment.

"Yes. The other set was a little worse for the wear."

"A bowtie?"

"I rather like it, don't you? I think it suits me."

Amy chuckled, slightly. Her face grew serious. "Why are you here?"

The Doctor took a deep breath. "Well... to be honest, I was hoping you would want to come with me."

Amy suddenly grew suspicious. "Where?"

"Anywhere. My ship can travel through space as well as time."

Amy paused a moment, processing this. "Why me?"

"Honestly, I've grown rather fond of you. I do hope we can be friends. And... I've lost my other friends."

"What do you mean?"

"I've been having some trouble with memory lately. I remember they were traveling with me, but then they weren't. I can't remember what happened, and I could use your help in finding them."

"Is that all? Just... friends?"

The Doctor frowned. "What else would it be?"

Amy didn't respond. "Wouldn't your box be a bit small for the two of us?"

"Oh." He smiled, mischievously. "You would be surprised." He turned the key in the lock and opened the door.

Light streamed out of the doorway. There was an audible humming sound came floating out from inside.

Amy was transfixed. She slowly stepped inside, marveling at the spacious room she found.

"It's called the Tardis. Time And Relative Dimensions In Space." The Doctor slipped in behind her, beaming. "It's my home."

"You're an Alien." She turned toward him.

"I suppose so. Does that bother you?"

"No."

"Good." The Doctor checked the controls. "It's all functioning properly now. It's ready to go if you want to."

"Can you get me back for tomorrow?" Amy turned around in a circle, eyes wide.

The Doctor didn't respond at first. "Well, yes, I suppose."

Amy turned toward him, an excited smile on her face. "Where will we go first?"

The Doctor clapped his hands together and smiled. Then he began working the controls, setting dials and pressing buttons.

The center column began to rise and fall, and the strange wheezing, groaning sound filling the room.

Outside, the wind picked up slightly, and the box slowly faded into nothing.

* * *

AN: There you have it! Now that I've finally gotten through this story for the second time, I'm happy to say that I can finally move on to the next story and the introduction of another companion: Jamie McCrimmon!

I'd love any feedback about the rewrite! All reviews are welcomed and loved! Let me know if there are any issues with grammar and writing!

Until the next time!

The Pygairian


	4. A moment in between

The Doctor's eyes drifted over the familiar controls. Everything he saw was new to his eyes. He gently ran his hand over the smooth surface. The gentle humming of the Tardis tickled the back of his consciousness.

He looked at his reflection on one of the monitors. He had never been good at judging physical attraction in faces before, but he liked to think the new unfamiliar face he saw staring back at him was handsome. It was still unfamiliar.

He chuckled as he remembered that he had passed by a mirror in the hall and had nearly had a heart attack when he saw himself.

He had also cut himself while shaving this morning. He still wasn't used to this facial structure. His previous face had been thin and smooth, not the strong jaw and harsh creases he had now.

He looked at his hands. They were strong, with thicker fingers, yet he knew somehow they would be more gentle.

The Doctor closed his eyes, and searched his mind. He had never done this before, and he knew that, of course. But as he had never done it before, he had never realized how much of him would be changed. He now looked back at many things The Old Man had done or said and found those actions strange and unnatural. He had changed more than his appearance.

His memory was still a little spotty, but he had remembered a little more. The Cybermen, and the Arctic base. His empty sort of feeling he had begun to have, and the feeling as if his hearts were slowing. He had lived in that body a long while, and assumed it had been old age, but now he wasn't sure. He was, after all, only about 450 years old. He frowned.

He moved to the far side of the console and began setting coordinates. He let his hands guide themselves, and he found they were already accustom to and comfortable with the controls. They seemed to know where to go before he knew, and he marveled at this.

"Doctor?"

He turned around to see Any standing in the doorway to the hall. She had changed into a short skirt and a red jumper.

"Hello, Amy!" He said, cheerily. "Are you ready? We should be there in about ten minutes."

Her eyes narrowed. "Where exactly are we going?"

The Doctor smiled. "The Tardis has a mind of her own. She always takes me where I need to be."

Amy frowned slightly, but didn't respond.

A light turned on on the console, and the Doctor began the landing sequence, his new hands moving smoothly across the various parts. The grinding sound of the time rotor began, and in a moment, the Tardis had landed.

The Doctor flipped a switch, bringing a picture up on the scanner. It showed a dense forest, with fog drifting throughout the branches and undergrowth. There was hardly a sign of life.

"That looks like Scotland." Amy said, surprise in her voice.

"It may be. The readings show it has the same atmosphere concentration as earth. Let's go take a look, shall we?"

"Okay."

The Doctor opened the door. Gentle mist drifted in.

"It certainly looks like Scotland from here. The only question is when?" The Doctor pulled his cloak off the coat rack near the door and put it on. He took a poncho down and handed it to Amy. "It might be a little chilly. Take this."

Amy looked at it, somewhat dubiously, but accepted it.

With that, he led the way outside, closing the door behind them.


	5. The Highlanders Pt 1

The woods were still, the mist drifting lazily along the ground. Faintly, somewhere off in the far distance, a gunshot was heard.

A grinding sound very suddenly echoed through the woods. A tall blue box began to materialize. As soon as it became solid, the door opened, and a man and a girl exited.

The Doctor looked around, taking in his surroundings.

Amy walked a little way off, looking at the trees and plants. Something caught her eye. "Doctor!"

The Doctor approached her, looking where she pointed. "It looks like an eighteenth-century cannonball." He said, inspecting it closer. He touched it, only to pull his hand away quickly, and put his finger in his mouth, frowning. "Likely fired recently. It's still hot."

Amy looked around. "Where did it come from?"

"Judging by the damage to the undergrowth, it appears to have come from that direction." The Doctor pointed. He furrowed his brow, resting a hand on his chin.

"Let's go see." Amy started off in the direction that the Doctor had indicated.

"Amy..." The Doctor hesitated, and then followed her. Something about this place was giving him a bad feeling.

Amy climbed up the steep slope quickly, standing at the top and surveying the area around it. There was a moor at the foot of the hill, with trees around the edges. nestled in a grove was a small lifeless cottage.

The Doctor caught up to her. "There's our culprit," he said, pointing down toward the nearby Moor.

Amy followed his finger until her eyes rested on a cannon sitting among some bushes.

"Let's take a look." The Doctor started down.

Amy followed more slowly. She observed her surroundings, a tinge of disbelief resting at the back of her thoughts. None of this should be possible, yet here she was.

"Amy!"

She looked down where the Doctor was standing next to the cannon, and quickened her pace. "What is it?"

"This is a cannon from the mid-eighteenth century, just like the cannonball near the Tardis. But look at it. It's been spiked." The Doctor rested a hand on his chin, motioning with his other hand at the mouth of the cannon. It had a rough metal spike driven through it to prevent its use. "I wonder..."

"Do nae move!" Very suddenly, there was a cold steel blade pointed at the two of them. Two young men, one looking as if he were hardly nineteen, stood in front of them. Both wore tartan kilts, and looked worse for the wear, with dirt smudges, bruises, and scrapes covering them. Both held blades pointed at Amy and the Doctor.

The Doctor stepped in front of Amy, lifting his hands in surrender. "We don't mean any harm."

"Doctor..." Amy moved slightly closer to him.

The older of the two spat. "Ye filthy sasanach! We willnae fall for your lies!"

"Aye!" The younger one agreed.

The older one continued. "We ken why ye came 'ere."

"Aye!"

The older of the two cast a silencing glance at the other. Then he continued. "Ye'll be comin' with us now." He ushered the Doctor and Amy forward, toward the cottage, keeping the point of his sword on the Doctor's back.

When they got there, they pushed them roughly inside.

There was a single room, with a fireplace that was cold, a table, and a cot in the corner. An older looking gentleman lay on it.

"There must be some sort of misunderstanding." The Doctor started to say.

"Shut yer mouth!" the older one hissed, moving his sword closer.

"Alec? Jamie?" A young woman, hardly seventeen, drew their attention to herself. "Ye brought them here? What were ye thinkin'? They've probably go' Redcoats on their tails!"

"Do nae fash yourself, Kirsty. We made sure nae to be followed. " The older on, Alec, responded.

"Excuse me, but-..." The Doctor began.

"Nae a word out of ye!" Hissed Jamie, the younger one, pointing his knife at the Doctor's throat. "We willnae let ye harm the Laird."

"Harm?" The Doctor sounded exasperated. "Why would we do that? We don't even know who you are!"

"Lies!" Alec hissed. "I ought tae run ye through right here an' now!"

"Alec... Jamie..." The old man on the cot groaned. "Give them a chance tae pray to God for forgiveness..."

"Forgiveness?" The Doctor's eyes widened. "For what?"

Amy was just as frustrated as the Doctor. These men, whoever they were, seemed bent on killing them, even though they hadn't done a thing, but she had a nasty suspicion that she knew why. They needed some way out of this situation, and quick. She looked around for anything that she could use and noticed sitting on the table was an old flintlock pistol.

She grasped the pistol and whipped it up, leveling it at the two men threatening the Doctor. They froze, stunned.

"Get back against the wall!" She commanded, in a loud voice.

They obeyed, but not before Jamie whispered, in shock, "She's Scottish!"

"Well done, Amy." The Doctor said. "Now. If you two would hand over your weapons..."

Jamie and Alec did as they were told, handing their weapons to the Doctor.

"Now..." The Doctor turned to the man on the bed. "I can see this man has been wounded badly, and as you three most likely don't want him to bleed to death, I suggest you do as I say. I'll need some clean water."

"Kirsty..." Alec motioned for her to go.

"I dinna want tae to leave him!" She protested.

"Amy, go with her. I trust if we put the gun down, you two will not molest us?" The Doctor raised an eyebrow at Jamie and Alec, smiling gently. "We only want to help, you know."

The two of them looked at each other a moment.

"Aye," Alec said, nodding.

"Amy, you may put the gun down."

"Doctor..."

"A Scotsman's word is his honor." The Doctor smiled.

Reluctantly, Amy tossed the gun to the table, only for it to fire suddenly.

"What are the tryin' tae do? Bring the Redcoats down on us?" Alec hissed.

Amy stared at the gun. "I-it was an accident!"

"It's alright Amy." The Doctor said. He was bent over the Laird, inspecting the wound. "Go fetch some water, there's a good girl."

"I'll show ye the way," Kirsty said, leading Amy out of the house.

Alec and Jamie watched the Doctor closely.

"Can ye do anything for him?" Jamie asked.

The Doctor continued to inspect the wound. "Yes, I... I think so. It will take some time though."

"Aye, well, we dinnae have any." Alec looked out the window. "Redcoats! The must 'ave heard the shot."

"What d'we do?" Jamie asked.

"There's nae a reason they should ken there are more that one of us here," Alec said. "I'll go out and draw them off. After they've gone, ye try to get the Laird and Kirsty to safety. I'll try to join ye as soon as possible." He took Jamie by the arm. "Promise ye'll keep them safe."

Jamie nodded. "Aye. I will."

"Don't go out there!" The Doctor hissed. "You'll only get yourself killed!"

"I've got a chance!" Alec responded.

"No, you haven't!" the Doctor's voice was forceful. "The redcoats will gun you down the moment you set foot outside. Jamie is a strong lad, but he can't protect Kirsty _and _your Laird. You'll leave them defenseless!"

Alec seemed uncertain for a moment. "Nae, it's what I need tae do." He turned to the door, but before he could the door burst open.

English soldiers pushed their way in, pointing their guns at all the occupants. A more decorated soldier came forward, observing them. He eyed the Doctor, interestedly.

"You don't look like a rebel." He said. "A deserter?"

The Doctor's eyes narrowed, but he didn't respond.

The lieutenant shrugged. "No matter. You'll hang with the rest of them."

* * *

AN: Sorry for the long wait. I've been mostly working on another story of mine, and I'd sort of forgotten about this one. Let me know what you think of this chapter! I'd love to hear your feedback. Also, if you have any suggestions for what stories you'd like to see, from the second Doctor's era, or the Eleventh Doctor's, let me know. I can't guarantee anything, but I'd love to know what you guys would like.


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